[2023-03-17 09:33:11,144] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:33:11,144] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:33:11,144] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd7669e9-8fe4-45f2-8b3c-0cef8aec7928/dqc_reference
[2023-03-17 09:33:12,227] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:33:12,227] [INFO] Task started: Prodigal
[2023-03-17 09:33:12,227] [INFO] Running command: cat /var/lib/cwl/stg7172192b-384f-4aca-aaa5-fb2cf4bc0f86/OceanDNA-a775.fa | prodigal -d OceanDNA-a775/cds.fna -a OceanDNA-a775/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:33:18,296] [INFO] Task succeeded: Prodigal
[2023-03-17 09:33:18,297] [INFO] Task started: HMMsearch
[2023-03-17 09:33:18,297] [INFO] Running command: hmmsearch --tblout OceanDNA-a775/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd7669e9-8fe4-45f2-8b3c-0cef8aec7928/dqc_reference/reference_markers.hmm OceanDNA-a775/protein.faa > /dev/null
[2023-03-17 09:33:18,409] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:33:18,410] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg7172192b-384f-4aca-aaa5-fb2cf4bc0f86/OceanDNA-a775.fa]
[2023-03-17 09:33:18,427] [INFO] Query marker FASTA was written to OceanDNA-a775/markers.fasta
[2023-03-17 09:33:18,427] [INFO] Task started: Blastn
[2023-03-17 09:33:18,427] [INFO] Running command: blastn -query OceanDNA-a775/markers.fasta -db /var/lib/cwl/stgfd7669e9-8fe4-45f2-8b3c-0cef8aec7928/dqc_reference/reference_markers.fasta -out OceanDNA-a775/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:18,849] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:18,857] [INFO] Selected 5 target genomes.
[2023-03-17 09:33:18,858] [INFO] Target genome list was writen to OceanDNA-a775/target_genomes.txt
[2023-03-17 09:33:18,873] [INFO] Task started: fastANI
[2023-03-17 09:33:18,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg7172192b-384f-4aca-aaa5-fb2cf4bc0f86/OceanDNA-a775.fa --refList OceanDNA-a775/target_genomes.txt --output OceanDNA-a775/fastani_result.tsv --threads 1
[2023-03-17 09:33:20,681] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:20,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd7669e9-8fe4-45f2-8b3c-0cef8aec7928/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:33:20,681] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd7669e9-8fe4-45f2-8b3c-0cef8aec7928/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:33:20,686] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:33:20,686] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:33:20,686] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.7417	300	385	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	81.3148	310	385	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	81.236	293	385	95	below_threshold
Nitrosopumilus maritimus	strain=SCM1	GCA_000018465.1	338192	338192	type	True	80.8646	287	385	95	below_threshold
Nitrosopumilus piranensis	strain=D3C	GCA_000875775.1	1582439	1582439	type	True	80.8624	289	385	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:33:20,686] [INFO] DFAST Taxonomy check result was written to OceanDNA-a775/tc_result.tsv
[2023-03-17 09:33:20,687] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:33:20,687] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:33:20,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd7669e9-8fe4-45f2-8b3c-0cef8aec7928/dqc_reference/checkm_data
[2023-03-17 09:33:20,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:33:20,704] [INFO] Task started: CheckM
[2023-03-17 09:33:20,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a775/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a775/checkm_input OceanDNA-a775/checkm_result
[2023-03-17 09:33:42,549] [INFO] Task succeeded: CheckM
[2023-03-17 09:33:42,550] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:33:42,583] [INFO] ===== Completeness check finished =====
[2023-03-17 09:33:42,583] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:33:42,583] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a775/markers.fasta)
[2023-03-17 09:33:42,583] [INFO] Task started: Blastn
[2023-03-17 09:33:42,583] [INFO] Running command: blastn -query OceanDNA-a775/markers.fasta -db /var/lib/cwl/stgfd7669e9-8fe4-45f2-8b3c-0cef8aec7928/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a775/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:43,884] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:43,885] [INFO] Selected 5 target genomes.
[2023-03-17 09:33:43,885] [INFO] Target genome list was writen to OceanDNA-a775/target_genomes_gtdb.txt
[2023-03-17 09:33:44,226] [INFO] Task started: fastANI
[2023-03-17 09:33:44,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg7172192b-384f-4aca-aaa5-fb2cf4bc0f86/OceanDNA-a775.fa --refList OceanDNA-a775/target_genomes_gtdb.txt --output OceanDNA-a775/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:33:46,013] [INFO] Task succeeded: fastANI
[2023-03-17 09:33:46,017] [INFO] Found 5 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-17 09:33:46,018] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002317795.1	s__Nitrosopumilus sp002317795	96.1991	360	385	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_001543015.1	s__Nitrosopumilus sp001543015	95.9883	354	385	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_013215285.1	s__Nitrosopumilus sp013215285	83.6606	318	385	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510275.1	s__Nitrosopumilus sp001510275	82.6902	299	385	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730325.1	s__Nitrosopumilus sp002730325	82.5544	277	385	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:33:46,018] [INFO] GTDB search result was written to OceanDNA-a775/result_gtdb.tsv
[2023-03-17 09:33:46,018] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:33:46,019] [INFO] DFAST_QC result json was written to OceanDNA-a775/dqc_result.json
[2023-03-17 09:33:46,019] [INFO] DFAST_QC completed!
[2023-03-17 09:33:46,019] [INFO] Total running time: 0h0m35s